We used three second-generation sequencing platforms to develop 12 microsatellite markers for Gray’s beaked whale (Mesoplodon grayi). There was a strong correlation between the amount of sequence obtained from each platform and the number of microsatellites recovered. In order to design reliable primers we found that it was important in all cases to eliminate low quality reads and trim sequences so that 80 % of each sequence had a PHRED score of >20. We found that tri- and tetranucleotide repeats produced less stutter enabling robust peak-calling and consistent genotyping. The microsatellites developed here will be useful for the population genetics and conservation studies of Gray’s beaked whales.